Swapnil Keshari

Activation of dermal mast cells through the Mas-related G protein–coupled receptor B2 receptor (MrgprB2 in mice and MrgprX2 in humans) is a key component of numerous inflammatory skin diseases, including dermatitis and rosacea. Sensory neurons actively suppress mast cell activation through the regulated release of glutamate, resulting in reduced expression of Mrgprb2 as well as genes associated with proteins found in mast cell granules. To determine whether exogenous glutamate receptor agonism could suppress mast cell function, we determined that mast cells have relatively selective expression of the glutamate receptor ionotropic, kainate 2 (GluK2). A GluK2-specific agonist, SYM2081, effectively inhibited mast cell degranulation in response to MrgprB2 agonism in both murine mast cells and human skin explants in vitro as well as in vivo after both intradermal and topical administration of SYM2081 to mice. Analyses of transcriptomic datasets from SYM2081-treated mast cells using standard differential expression approaches and an interpretable machine learning technique revealed a previously unrecognized cellular program coordinately regulated by GluK2 agonism. GluK2 agonism suppressed the expression of Mrgprb2 and genes associated with mast cell proliferation. Suppression of mast cell proliferation by SYM2081 exposure was confirmed on the basis of reduced Ki-67 expression and BrdU incorporation in vitro and in vivo. Last, pretreatment with SYM2081 reduced skin inflammation in murine models of dermatitis and rosacea. Thus, agonism of GluK2 represents a promising approach to suppress mast cell activation and may prove beneficial as therapy for inflammatory diseases in which mast cell activation is pathogenic.

SUMMARY Antibody responses are determined by activated B cells bifurcating into plasmablasts (PBs) and germinal center B cells (GCBCs). Gene regulatory networks (GRNs) underlying human B cell fate choice remain uncharted. Temporally resolved single-cell multi-omics, computational modeling and CRISPR-based perturbations were used to assemble, simulate and test high-resolution GRNs underlying PB and GC fates. The results converged with orthogonal predictions of transcription factor (TF) action at single-nucleotide resolution, revealing dominant and reciprocal actions of IRF4 and its binding partners at simple and composite IRF motifs. Single-cell perturbation analysis of these TFs demonstrated multiple reciprocal negative feedback loops controlling the bifurcation. Additionally, IRF4 and BLIMP1, co-repressed the cell cycle regulators MYC and CCND2 . G0/G1 lengthening accelerated the switching of cells to an IRF4 hi BLIMP1 hi regulatory state and enhanced the probability of PB specification, thereby uncovering a self-reinforcing regulatory module that couples cell cycle dynamics to B cell fate choice.

Germinal center B cell responses are defined by many positive regulators of affinity maturation, but few components that restrain clonal dominance, notably Nr4a1, are known. We reveal an unsuspected role for BLIMP1 (Prdm1)—a plasma cell determinant—as a feedback regulator of affinity maturation. Single-cell RNA and B cell receptor (BCR) sequencing showed that B cell-specific Prdm1 loss drives an exaggerated germinal center reaction with larger clones, increased somatic hypermutation and greater clonal dominance, independent of Nr4a1. Single-cell chromatin profiling with base-resolution modeling indicated that Blimp-1 represses expression of BCR-signaling genes, gating chromatin accessibility at interferon-stimulated response elements, Ets–interferon regulatory factor composite elements, nuclear factor kappa B and Oct motifs. In the absence of BLIMP1, enhanced BCR-signaling augments activities of transcription factors that promote G1–S transition during light zone (LZ) selection and fuel dark zone (DZ) expansion. Thus, BLIMP1 attenuates BCR signaling and constrains the LZ to DZ transition, fine-tuning clonal competition, thereby maintaining repertoire diversity. Singh and colleagues identify a role for the transcription factor BLIMP1, encoded by Prdm1, in the regulation of germinal center responses. They show that BLIMP1 acts as a negative feedback regulator of B cell affinity maturation and clonal dominance.

Abstract An exponential growth in the scientific literature necessitates the development of highly scalable computational tools that can effectively analyze and distill insights from complex, interconnected research landscapes. We introduce Distributed, Interpretable, and Scalable computing for Co-authorship Networks (DISCo-Net), a robust and scalable tool engineered to curate and examine large-scale co-authorship networks by harnessing the power of distributed computing and advanced relational database queries. We use DISCo-Net to analyze co-authorship networks derived from millions of papers in the life sciences and physical sciences over more than two decades. Using a range of deep learning approaches, we surprisingly found that pre-trained zero-shot embeddings from a sentence transformer better captured global co-authorship relationships than a complex graphical attention transformer. Even more surprisingly, a simple interpretable Term Frequency-Inverse Document Frequency (TF-IDF) model performed as well as the Bidirectional Encoder Representations from Transformers (BERT) model. Through topic modeling on TF-IDF document descriptors, we identified nine major research areas prevalent globally over the past 24 years and captured topic-specific shifting trends in scientific output. Our study draws an innovative parallel between collaborative research networks and genomic regulatory structures, applying genomics data analysis methodologies to uncover patterns in global scientific collaboration. This approach reveals interpretable alignments between research interests and human developmental stages, while also identifying emerging influential players in the global research landscape. The findings highlight potential far-reaching consequences of current funding challenges, particularly in the U.S., and offer actionable insights for optimizing resource allocation and fostering innovation in an interconnected global scientific community.

Abstract It has been recently appreciated that mast cells respond to glutamate in the context of neural transimtter release and tissue injuries. However, the precise subtype of glutamate receptor expressed on dermal mast cells at steady states and its function remain to be elucidated. Herein, we identified the kainate receptor GluK2/KA2 as the predominant glutamate receptor expressed on dermal MCs at the mRNA and protein level. GluK2 agonists such as glutamic acid and kainic acid suppressed the activation of cultured peritoneal mast cells (PMCs) in response to MrgprB2 ligand compound 48/80, corroborating a previously demonsrated neuroimmune pathway. The GluK2 selective agonist SYM2081 downregulated MrgprB2 expression and inhibited compound 48/80-mediated PMC activation. SYM2081 suppresed various mast cell-dependent inflammation models in vivo, such croton oil-induced irritant dermatitis, DNFB contact hypersensitivity, and LL-37 induced rosacea. The suppressive effect of SYM2081 on mast cells holds true in a model of human skin explants as well. Transcriptomic analysis revealed that GluK2 agonism suppresses proliferation pathways in mast cells and downregulates granule content synthesis, such as mast cell chymase 1. Together, this study identified a previously unappreciated glutamate receptor on dermal mast cells and raised the interesting posibility of using selective GluK2 agonists to as a therapeutic agent for inflammatory conditions where MCs play a key role in the pathogenesis.